Contacts of the helix formed by residues 576 - 590 (chain N) in PDB entry 5L4K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 576 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542N GLU* 4.9 11.9 - - - +
545N LEU* 6.4 0.2 - - + -
574N LYS 3.9 4.7 - - - +
575N ASP* 1.3 85.1 - - + +
577N ILE* 1.3 74.6 + - + +
578N LEU 3.2 0.2 - - - -
579N ARG* 3.5 14.6 - - - +
580N ARG* 3.0 27.4 + - - +
611N ASN* 3.6 38.4 - - - +
613N ASP* 3.8 19.0 - - + +
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Residues in contact with ILE 577 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541N HIS 4.8 2.9 - - - +
542N GLU* 4.8 17.0 - - - +
545N LEU* 3.1 59.2 - - + +
546N ARG* 3.8 24.7 - - + +
549N ALA* 3.4 16.1 - - + +
575N ASP* 3.4 1.3 - - + +
576N PRO* 1.3 84.7 - - + +
578N LEU* 1.3 63.8 + - + +
580N ARG* 4.0 18.1 - - - +
581N SER* 3.0 29.3 + - - -
613N ASP* 4.2 6.7 - - - +
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Residues in contact with LEU 578 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533N VAL* 5.0 9.0 - - + -
536N ALA* 4.0 31.0 - - + +
537N GLN* 3.4 38.4 - - - +
545N LEU* 5.1 2.7 - - + -
549N ALA* 6.1 0.9 - - + -
552N ILE* 5.7 5.2 - - + -
570N LEU* 3.3 40.0 - - + +
573N ASP* 4.1 26.2 - - + +
575N ASP* 3.8 17.9 + - + -
576N PRO 3.2 0.4 - - - -
577N ILE* 1.3 86.0 - - + +
579N ARG* 1.3 60.7 + - - +
581N SER* 4.6 7.4 - - - -
582N GLY 3.6 7.0 + - - -
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Residues in contact with ARG 579 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570N LEU 4.0 8.3 - - - +
571N CYS* 3.7 20.8 - - - +
572N ARG* 4.8 3.1 - - - +
573N ASP 3.2 21.0 + - - +
574N LYS* 3.3 12.7 + - - +
575N ASP 2.4 36.0 + - - +
576N PRO* 3.3 20.0 + - - +
578N LEU* 1.3 77.3 - - - +
580N ARG* 1.3 64.2 + - - +
582N GLY 3.1 4.4 + - - -
583N MET* 3.0 26.5 + - - +
602N LEU* 6.4 0.2 - - + -
605N VAL* 6.3 1.3 - - - -
609N ASP* 3.8 37.4 + - - +
611N ASN* 4.3 9.3 - - - +
613N ASP* 5.4 0.2 - - - +
614N VAL* 4.0 20.1 - - + +
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Residues in contact with ARG 580 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546N ARG* 3.6 28.3 + - - +
549N ALA* 5.6 5.4 - - + +
550N VAL* 5.9 1.6 - - - +
576N PRO 3.0 17.8 + - - +
577N ILE* 4.0 12.8 + - - +
579N ARG* 1.3 73.2 - - - +
581N SER* 1.3 66.6 + - - +
583N MET* 2.8 15.9 + - - +
584N TYR* 2.8 30.6 + - + -
612N ASP* 5.2 2.8 + - - -
613N ASP* 2.8 61.0 + - + +
614N VAL* 4.6 1.3 - - - +
616N ARG* 6.4 0.6 - - - +
617N ALA* 4.1 7.3 - - + +
770N TRP* 3.1 56.3 - - - +
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Residues in contact with SER 581 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549N ALA* 3.2 37.6 + - - +
552N ILE* 4.0 19.5 - - - +
553N ALA* 4.3 1.9 + - - -
570N LEU* 5.5 2.7 - - - -
577N ILE 3.0 19.3 + - - -
578N LEU* 4.6 7.6 - - - -
580N ARG* 1.3 76.5 - - - +
582N GLY* 1.3 52.5 + - - +
583N MET 2.8 10.7 + - - -
584N TYR* 3.0 19.6 + - - -
585N THR* 3.1 19.2 + - - +
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Residues in contact with GLY 582 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567N ILE* 3.2 18.9 - - - +
570N LEU* 4.1 20.6 - - - +
571N CYS* 3.3 8.9 - - - -
578N LEU 3.6 14.8 + - - -
579N ARG 3.1 14.1 + - - -
580N ARG 3.1 1.4 - - - -
581N SER* 1.3 75.3 - - - +
583N MET* 1.3 69.0 + - - +
585N THR* 4.6 4.9 - - - +
586N VAL* 4.1 0.7 - - - +
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Residues in contact with MET 583 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567N ILE* 3.7 19.5 - - + -
571N CYS* 3.5 24.9 - - + -
579N ARG 3.0 8.7 + - - +
580N ARG* 2.8 8.8 + - - +
582N GLY* 1.3 83.5 - - - +
584N TYR* 1.3 59.9 + - - +
585N THR 3.4 1.1 - - - -
586N VAL* 3.5 11.5 + - - +
587N ALA* 3.0 24.1 + - - +
598N ALA* 4.3 9.2 - - - +
601N ARG* 3.9 25.4 - - + +
602N LEU* 3.4 48.5 - - + -
614N VAL* 5.9 0.9 - - + -
617N ALA* 5.7 7.2 - - + -
618N ALA* 5.9 2.0 - - - +
621N SER* 5.7 2.7 - - - -
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Residues in contact with TYR 584 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549N ALA* 6.0 1.8 - - + -
550N VAL* 6.2 1.8 - - + -
553N ALA* 3.4 26.7 - - + -
580N ARG* 2.8 40.3 + - + +
581N SER* 3.0 6.0 + - - +
583N MET* 1.3 74.8 - - - +
585N THR* 1.3 59.2 + - - +
587N ALA* 2.6 38.6 + - + +
588N MET* 3.0 15.7 + - + +
617N ALA* 4.1 13.0 - - + +
620N GLU* 3.0 29.9 + - - -
764N LEU* 4.0 25.4 - - + -
768N GLN* 3.1 23.0 + - - +
770N TRP* 3.0 29.3 + + - -
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Residues in contact with THR 585 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552N ILE* 4.5 6.8 + - + -
553N ALA* 4.2 18.2 - - - +
556N MET* 3.2 30.6 - - - +
563N ALA* 4.4 25.3 - - + +
564N ASP* 3.1 25.0 + - - +
567N ILE* 6.0 0.2 - - + -
570N LEU* 5.0 2.2 - - + -
581N SER 3.1 15.7 + - - +
582N GLY* 4.6 6.3 - - - +
584N TYR* 1.3 78.1 - - - +
586N VAL* 1.3 61.3 + - + +
588N MET* 3.3 0.9 + - - +
589N ALA* 3.0 30.5 + - - +
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Residues in contact with VAL 586 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564N ASP* 3.0 26.5 - - - +
567N ILE* 3.5 29.8 - - + -
582N GLY 4.1 8.1 - - - +
583N MET* 3.7 11.7 - - - +
584N TYR 3.1 0.6 - - - -
585N THR* 1.3 74.2 - - + +
587N ALA* 1.3 65.4 + - - +
588N MET 3.4 0.3 + - - -
590N TYR* 3.5 28.7 + - + +
595N ASN* 3.0 33.4 - - - +
598N ALA* 4.3 10.1 - - + -
601N ARG* 5.7 0.7 - - - +
625N ILE* 5.1 0.3 - - - +
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Residues in contact with ALA 587 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583N MET 3.0 13.8 + - - +
584N TYR* 2.6 31.8 + - + +
586N VAL* 1.3 74.1 - - - +
588N MET* 1.3 68.8 + - + +
590N TYR 3.9 14.0 - - - +
591N CYS* 3.9 5.4 + - - +
620N GLU* 6.0 0.4 - - - +
621N SER* 4.8 24.2 - - - +
624N PHE* 4.6 8.1 - - + +
625N ILE* 4.0 14.8 - - + +
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Residues in contact with MET 588 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553N ALA* 4.3 17.3 - - + +
554N LEU* 5.5 5.8 - - + -
556N MET 3.3 23.7 - - - +
557N TYR* 3.8 15.6 - - + -
584N TYR* 3.0 21.9 + - + +
585N THR 4.3 1.6 - - - +
587N ALA* 1.3 84.5 - - + +
589N ALA* 1.3 63.9 + - - +
590N TYR 3.3 1.0 + - - -
591N CYS* 3.8 18.0 + - - +
624N PHE* 3.5 53.4 - - + -
760N VAL* 4.4 13.7 - - + -
764N LEU* 3.5 25.4 - - + -
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Residues in contact with ALA 589 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556N MET* 3.9 16.3 + - + +
558N GLY* 3.1 33.0 - - - +
560N MET* 3.6 37.8 - - - +
564N ASP* 4.2 7.9 - - - +
585N THR 3.0 17.8 + - - +
588N MET* 1.3 77.4 - - - +
590N TYR* 1.3 63.4 + - + +
591N CYS 3.5 2.0 + - - +
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Residues in contact with TYR 590 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N MET* 3.3 48.8 - - + +
561N GLU* 4.6 11.9 + - + +
564N ASP* 4.1 16.2 - - - -
586N VAL* 3.5 22.0 + - + +
587N ALA 3.9 4.0 - - - -
588N MET 3.3 0.2 - - - -
589N ALA* 1.3 79.6 - - + +
591N CYS* 1.3 59.9 + - - +
592N GLY 3.8 0.9 + - - -
593N SER* 3.4 25.5 + - - +
595N ASN* 3.4 31.1 - - - +
625N ILE* 3.5 20.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il